Re: [PyMOL] WARNING: glDrawBuffer caused GL error help
Hello Tom, Have you tried this workaround to suppress the OpenGL warnings? https://sourceforge.net/p/pymol/mailman/message/32035245/ PyMOL>feedback disable, opengl, warnings Are there any rendering issues besides the warnings flooding the console? Does the graphics look normal? Thanks! Piotr On Sun, Dec 18, 2016 at 3:28 PM, Thomas Laughlin wrote: > Hello, > > I installed unofficial PyMOL 1.8.5.0 using Anaconda2 on a windows 10 > machine possessing a Nvidia Quadro K620. > > In the PyMOL command window, the text "WARNING: glDrawBuffer caused GL > error" is repetitively printed which makes its nearly impossible to see > other output or the help. > > I've installed unofficial PyMOL on other machines without dedicated graphics > cards and never observed this. > I saw a previous posted about this from 2014, but it doesn't list a > solution. > > Any help is appreciated. > > Best, > > -Tom > > > Thomas G. Laughlin III > PhD MCB (BBSB, Student) | Univ. of California-Berkeley | Present > BS Biochemistry | Univ. of Missouri-Columbia | 2014 > thomas.laughlin...@gmail.com > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/intel ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] WARNING: glDrawBuffer caused GL error help
Yes, you should be able to use PyMOL "File" -> "Edit pymolrc" and add the command there: feedback disable, opengl, warnings It creates a file named .pymolrc (note the initial dot) in your home directory (C:\Users\ by default on Win 7/8/10). Then the command should be executed on startup. - Piotr On Mon, Dec 19, 2016 at 11:20 AM, Thomas Laughlin wrote: > Yes, but the work around works for a single session. > Is there a start-up script to add it to? > > > Graphics look normal. > > Thomas G. Laughlin III > PhD MCB (BBSB, Student) | Univ. of California-Berkeley | Present > BS Biochemistry | Univ. of Missouri-Columbia | 2014 > thomas.laughlin...@gmail.com > > On Mon, Dec 19, 2016 at 7:55 AM, Piotr Rotkiewicz > wrote: >> >> Hello Tom, >> >> Have you tried this workaround to suppress the OpenGL warnings? >> >> https://sourceforge.net/p/pymol/mailman/message/32035245/ >> >> PyMOL>feedback disable, opengl, warnings >> >> Are there any rendering issues besides the warnings flooding the >> console? Does the graphics look normal? >> >> Thanks! >> Piotr >> >> >> >> >> >> On Sun, Dec 18, 2016 at 3:28 PM, Thomas Laughlin >> wrote: >> > Hello, >> > >> > I installed unofficial PyMOL 1.8.5.0 using Anaconda2 on a windows 10 >> > machine possessing a Nvidia Quadro K620. >> > >> > In the PyMOL command window, the text "WARNING: glDrawBuffer caused GL >> > error" is repetitively printed which makes its nearly impossible to see >> > other output or the help. >> > >> > I've installed unofficial PyMOL on other machines without dedicated >> > graphics >> > cards and never observed this. >> > I saw a previous posted about this from 2014, but it doesn't list a >> > solution. >> > >> > Any help is appreciated. >> > >> > Best, >> > >> > -Tom >> > >> > >> > Thomas G. Laughlin III >> > PhD MCB (BBSB, Student) | Univ. of California-Berkeley | Present >> > BS Biochemistry | Univ. of Missouri-Columbia | 2014 >> > thomas.laughlin...@gmail.com >> > >> > >> > -- >> > Check out the vibrant tech community on one of the world's most >> > engaging tech sites, SlashDot.org! http://sdm.link/slashdot >> > ___ >> > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) >> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > -- Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today.http://sdm.link/intel ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] White color bar
Hello Kimberly,
Please try using [blue, white, red] in ramp_new:
cmd.ramp_new("ramp_obj", "ca_obj", range=[minval, maxval],
color="[blue,white,red]")
ramp_new recognizes only a limited set of pre-defined palettes (see
https://pymolwiki.org/index.php/Ramp_New ) and they need to be
specified without the brackets, e.g.
cmd.ramp_new("ramp_obj", "ca_obj", range=[minval, maxval], color="rainbow")
Thanks,
Piotr
On Tue, Feb 7, 2017 at 11:31 PM, Kimberly Jesseman
wrote:
> Hello,
>
>
> I have successfully colored the surface of a PDB by b factors I replaced by
> modifying the loadBfacts script. However, my color bar is only showing up
> as white instead of accurately showing the blue-white-red color scheme of my
> PDB (I've attached a picture). This is my script:
>
>
> from pymol import cmd, stored, math
>
>
> def loadBfacts (mol,startaa=1,source="newBfactors.txt"):
>
> """
>
> Replaces B-factors with a list of values contained in a plain txt file
>
>
> usage: loadBfacts mol, [startaa, [source, [visual]]]
>
>
>
> mol = any object selection (within one single object though)
>
> startaa = number of first amino acid in 'new B-factors' file (default=1)
>
> source = name of the file containing new B-factor values
> (default=newBfactors.txt)
>
>
>
> example: loadBfacts 1LVM and chain A
>
> """
>
> obj=cmd.get_object_list(mol)[0]
>
> cmd.alter(mol,"b=-1.0")
>
> inFile = open(source, 'r')
>
> counter=int(startaa)
>
> bfacts=[]
>
>
> for line in inFile.readlines():
>
> bfact=float(line)
>
> bfacts.append(bfact)
>
> cmd.alter("%s and resi %s"%(mol,counter), "b=%s"%bfact)
>
> counter=counter+1
>
>
> minval = min(bfacts)
>
> maxval = max(bfacts)
>
> cmd.show_as("surface",mol)
>
> cmd.spectrum("b","blue_white_red", "%s and n. CA"%mol, minimum=minval,
> maximum=maxval)
>
> cmd.create("ca_obj", mol + " and n. ca")
>
> cmd.ramp_new("ramp_obj", "ca_obj", range=[minval, maxval],
> color="[blue_white_red]")
>
> cmd.set("surface_color", "ramp_obj", mol)
>
>
> cmd.extend("loadBfacts", loadBfacts);
>
>
> Any insight into why this is occurring and how to fix it would be greatly
> appreciated.
>
> Thank you!
>
>
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
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Re: [PyMOL] Outline width for ray tracing
Hi Marko, You may want to tweak ray_trace_gain setting: https://pymolwiki.org/index.php/Ray_Trace_Gain - Piotr On Thu, May 25, 2017 at 6:53 AM, Marko Hyvonen wrote: > Hello Pymolers, > > I seem to fail to find the setting (which I recall having used before) > to get stronger/thicker outlines in ray traced images when using mode 1, > 2 and 3, in particular when rendering larger images. The lines seem to > be defined as pixels, as they get thinner the bigger the image is. Is is > possible to define this, and if so, how? > > many thanks in advance, Marko > > -- > > Marko Hyvonen > Department of Biochemistry, University of Cambridge > mh...@cam.ac.uk > +44-(0)1223-766 044 > @HyvonenGroup > http://www-cryst.bioc.cam.ac.uk/groups/hyvonen > > > > -- > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > ___ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net -- Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
